Variant report

Variant	rs12553213
Chromosome Location	chr9:100105428-100105429
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 121 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs1048451	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10521029	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs10817384	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10817491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10817504	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10981297	0.94[CEU][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap]
rs10981367	1.00[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs10981434	0.83[EUR][1000 genomes]
rs10981444	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10981460	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10981688	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10981701	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10981784	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10981801	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1123379	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11581	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs12115447	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12115448	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12377538	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12378350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12550923	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12551740	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12551818	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12552101	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12552659	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12553155	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12553259	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12554363	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12555277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13285567	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13286510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13287082	1.00[CEU][hapmap]
rs13289134	1.00[CEU][hapmap]
rs13289813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13292715	0.82[EUR][1000 genomes]
rs13300328	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13301045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13301965	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1531440	0.94[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1564048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1564050	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16919506	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16919656	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16919661	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16919671	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16919675	0.94[CEU][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1903635	0.81[JPT][hapmap]
rs1986462	0.94[CEU][hapmap]
rs2045729	1.00[CEU][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2045730	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2045731	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2279113	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2290933	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2306090	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2306092	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2306094	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2401384	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34135027	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34183765	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34355647	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34476799	0.82[EUR][1000 genomes]
rs34564795	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34609282	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34616426	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34754033	0.87[EUR][1000 genomes]
rs34870571	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34905303	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34954690	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35066943	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35123877	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35534888	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35623544	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35737497	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35778461	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35778718	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35788892	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3747490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3747491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3747492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3747495	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3747498	1.00[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3747499	1.00[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3747504	0.86[ASW][hapmap];1.00[CEU][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3747506	0.94[CEU][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3747507	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3747510	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3747511	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3827484	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3827485	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3994560	1.00[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4128763	1.00[CEU][hapmap]
rs41316960	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4742686	0.95[CHB][hapmap];0.88[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4743069	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4743070	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4743073	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4743082	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743083	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4743086	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60681062	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62557460	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62557461	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62557462	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62557463	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62559861	0.83[EUR][1000 genomes]
rs6478038	0.85[EUR][1000 genomes]
rs6478039	0.85[EUR][1000 genomes]
rs7020530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7038496	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7041222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73565808	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7859665	0.86[JPT][hapmap]
rs7872669	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7874652	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs898869	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs898870	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9696058	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762823	chr9:100083872-100105782	Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12553213	VN1R51P	cis	Thyroid	GTEx

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100070000-100131400	Weak transcription	Fetal Kidney	kidney
2	chr9:100077000-100106400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr9:100077000-100140800	Weak transcription	Fetal Brain Male	brain
4	chr9:100080400-100126400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr9:100083800-100124000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr9:100086400-100110400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr9:100086600-100121600	Weak transcription	Right Ventricle	heart
8	chr9:100086600-100132000	Weak transcription	Thymus	Thymus
9	chr9:100088000-100126200	Weak transcription	Primary B cells from peripheral blood	blood
10	chr9:100088200-100127000	Weak transcription	Duodenum Mucosa	Duodenum
11	chr9:100088600-100128600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr9:100088600-100132800	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr9:100088800-100121400	Weak transcription	Gastric	stomach
14	chr9:100089200-100128200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr9:100090600-100119000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr9:100090600-100133800	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr9:100091200-100106400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr9:100091600-100106400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr9:100091600-100149200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr9:100093000-100105600	Weak transcription	Fetal Lung	lung
21	chr9:100093000-100111000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr9:100093000-100117000	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr9:100093600-100106400	Weak transcription	Left Ventricle	heart
24	chr9:100093600-100122400	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr9:100094600-100109400	Weak transcription	Brain Angular Gyrus	brain
26	chr9:100095600-100116800	Weak transcription	Brain Hippocampus Middle	brain
27	chr9:100095800-100109200	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr9:100096800-100109400	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr9:100099000-100132200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr9:100101800-100105800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr9:100103200-100106400	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr9:100104000-100109600	Weak transcription	Primary B cells from cord blood	blood
33	chr9:100104400-100106000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr9:100104400-100107000	Strong transcription	Ovary	ovary
35	chr9:100104400-100109600	Weak transcription	Pancreas	Pancrea
36	chr9:100104400-100117000	Weak transcription	Colon Smooth Muscle	Colon
37	chr9:100104400-100118800	Weak transcription	Spleen	Spleen
38	chr9:100104400-100142000	Weak transcription	Rectal Smooth Muscle	rectum
39	chr9:100104600-100106000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr9:100104600-100109400	Weak transcription	Aorta	Aorta
41	chr9:100104600-100110400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr9:100104600-100111000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr9:100104600-100118200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr9:100104600-100128200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr9:100104800-100106400	Weak transcription	Fetal Muscle Leg	muscle
46	chr9:100104800-100107000	Strong transcription	Stomach Smooth Muscle	stomach
47	chr9:100104800-100116800	Weak transcription	Fetal Intestine Large	intestine
48	chr9:100105000-100106800	Strong transcription	Adipose Nuclei	Adipose
49	chr9:100105000-100111600	Weak transcription	Fetal Intestine Small	intestine
50	chr9:100105200-100105800	ZNF genes & repeats	Primary hematopoietic stem cells	blood

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